Comparative genomic hybridization (CGH) was first developed for genome-wide analysis of DNA sequence copy number in a single experiment, see, e.g., Pinkel (1998) Nat. Genet. 20:207-211. Genomic DNA microarray based comparative genomic hybridization (CGH) has the potential to solve many of the limitations of traditional CGH method, which relies on comparative hybridization on individual metaphase chromosomes. CGH can be used to determine the relative copy number of nucleic acid sequences between two samples. CGH can also be used to precisely map chromosomal abnormalities associated with disease.
In metaphase CGH, multi-megabase fragments of different samples of genomic DNA are labeled and hybridized to a fixed chromosome. See, e.g., Breen (1999) J. Med. Genetics 36:511-517; Rice (2000) Pediatric Hematol. Oncol. 17:141-147. The CGH can compare known or normal DNA to a test sample, e.g., DNA from a possible tumor cell. Signal differences between known and test samples are detected and measured. In this way, missing, amplified, or unique sequences in the test sample, as compared to “normal,” can be detected by the fluorescence ratio of normal control to test genomic DNA. In metaphase CGH, the target sites (on the fixed chromosome) are saturated by an excess amount of soluble, labeled genomic DNA.
In contrast to metaphase CGH, where the immobilized genomic DNA is a metaphase spread, in array-based CGH method the immobilized nucleic acids are arranged as an array, on, e.g., a biochip or a microarray platform. See, e.g., U.S. Pat. No. 5,830,645. Another difference is that in array-based CGH the immobilized genomic DNA is in molar excess as compared to the copy number of labeled (test and control) genomic nucleic acid. In array-based CGH, test and control, or “normal,” nucleic acids are mixed together and applied to the array, or “biochip.” In traditional CGH, because test and sample nucleic acids are mixed together before their application to the array they must be differentially labeled. Both the mixing together of samples and the use of different labels in the samples to be compared can result in artifacts and erroneous results.